September 14, 2012

ADMIXTOOLS alpha has been released

The ADMIXTOOLS software announced in Patterson et al. (2012) has now been released. The distribution includes the curated version of the HGDP set genotypes on the Affymetrix Human Origins Array in EIGENSTRAT format.

I made a quick test using data from the Li et al. version of the HGDP set that I'm most familiar with:

6 comments:

Hello Dienekes, could ask your advice on something. I'll be working on some hundreds of WGS (formatted as vcf, bam/sam, or even .fa) on which I'll want to run an analysis checking their ancestry, to make sure that people are (roughly) from where they say they are. As a simple example, we will want to determine whether a sample is primarily of European, East Asian, or African descent.

Of course, one could manually check each sample for a small number of unequally-MAF markers, but I expect there must be a smarter package already made for the task. What do you think?

The 26.5% inferred using the f4 ratio test is in great agreement with the 25.8% inferred by ADMIXTURE.

ADMIXTURE and f4 ratio seem to be much more in agreement with each other in their calculations of Negroid admixture in Caucasoids than in their calculations of Mongoloid admixture in Caucasoids. This must be because of the fact that Caucasoids are genetically much closer to Mongoloids than to Negroids and that, unlike f4 ratio, ADMIXTURE is not good at detecting ancient racial admixtures, especially between genetically relatively close races like Caucasoids and Mongoloids.

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